TY - JOUR
T1 - Defluorination Capability of l-2-Haloacid Dehalogenases in the HAD-Like Hydrolase Superfamily Correlates with Active Site Compactness
AU - Chan, Peter W. Y.
AU - Chakrabarti, Nilmadhab
AU - Ing, Chris
AU - Halgas, Ondrej
AU - To, Terence K. W.
AU - Wälti, Marielle
AU - Petit, Alain-Pierre
AU - Tran, Christopher
AU - Savchenko, Alexei
AU - Yakunin, Alexander F.
AU - Edwards, Elizabeth A.
AU - Pomès, Régis
AU - Pai, Emil F.
N1 - Funding Information:
We thank Julia Barette, Aiping Dong, Yan Liu, Max Wong, Xiaohui Xu and Hong Zheng for assistance with experiments. We are also grateful to the staff at beamline X8 C at the Brookhaven National Laboratory and at BioCARS and the Structural Biology Center – CAT, both at the Advanced Photon Source at Argonne National Laboratory, for their help during data collection. This work was supported by the Natural Sciences and Engineering Research Council of Canada through a graduate scholarship (PWYC) and operating grants to EAE (RGPIN‐2015‐06663) and EFP (RGPIN‐2015‐04877 and RGPIN‐2020‐068), by the Canada Research Chairs Program (EAE, EFP and RP), by a grant (MOP‐130461) from the Canadian Institutes for Health Research (RP), by the Government of Canada through Genome Canada and the Ontario Genomics Institute (2009‐OGI‐ABC‐1405; EAE, AS, AFY), and by the Protein Structure Initiative of the National Institutes of Health (Midwest Center for Structural Genomics, NIH grant GM074942; AS). Use of the National Synchrotron Light Source, Brookhaven National Laboratory, was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. DE‐AC02‐98CH10886. SBC‐CAT is operated by the University of Chicago Argonne, LLC, for the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research under contract DE‐AC02‐06CH11357. Use of the BioCARS Sector 14 was supported by the National Institutes of Health, National Center for Research Resources, under grant No. RR007707.
Publisher Copyright:
© 2021 Wiley-VCH GmbH
PY - 2022/1/5
Y1 - 2022/1/5
N2 - l-2-Haloacid dehalogenases, industrially and environmentally important enzymes that catalyse cleavage of the carbon-halogen bond in S-2-halocarboxylic acids, were known to hydrolyse chlorinated, brominated and iodinated substrates but no activity towards fluorinated compounds had been reported. A screen for novel dehalogenase activities revealed four l-2-haloacid dehalogenases capable of defluorination. We now report crystal structures for two of these enzymes, Bpro0530 and Rha0230, as well as for the related proteins PA0810 and RSc1362, which hydrolyse chloroacetate but not fluoroacetate, all at ∼2.2 Å resolution. Overall structure and active sites of these enzymes are highly similar. In molecular dynamics (MD) calculations, only the defluorinating enzymes sample more compact conformations, which in turn allow more effective interactions with the small fluorine atom. Structural constraints, based on X-ray structures and MD calculations, correctly predict the defluorination activity of the homologous enzyme ST2570.
AB - l-2-Haloacid dehalogenases, industrially and environmentally important enzymes that catalyse cleavage of the carbon-halogen bond in S-2-halocarboxylic acids, were known to hydrolyse chlorinated, brominated and iodinated substrates but no activity towards fluorinated compounds had been reported. A screen for novel dehalogenase activities revealed four l-2-haloacid dehalogenases capable of defluorination. We now report crystal structures for two of these enzymes, Bpro0530 and Rha0230, as well as for the related proteins PA0810 and RSc1362, which hydrolyse chloroacetate but not fluoroacetate, all at ∼2.2 Å resolution. Overall structure and active sites of these enzymes are highly similar. In molecular dynamics (MD) calculations, only the defluorinating enzymes sample more compact conformations, which in turn allow more effective interactions with the small fluorine atom. Structural constraints, based on X-ray structures and MD calculations, correctly predict the defluorination activity of the homologous enzyme ST2570.
KW - enzyme catalysis
KW - enzymic defluorination
KW - L-2-haloacid dehalogenases
KW - molecular dynamics
KW - protein structures
UR - http://www.scopus.com/inward/record.url?scp=85117465831&partnerID=8YFLogxK
U2 - 10.1002/cbic.202100414
DO - 10.1002/cbic.202100414
M3 - Article
C2 - 34643018
AN - SCOPUS:85117465831
SN - 1439-4227
VL - 23
JO - ChemBioChem
JF - ChemBioChem
IS - 1
M1 - e202100414
ER -